Skip to main content
SpringerLink
Log in

Bacterial Communities in Various Conditions of the Composting Reactor Revealed by 16S rDNA Clone Analysis and DGGE

  • Chapter
  • First Online:
Sustainable Biotechnology

Abstract

Composting is an efficient and cost-effective process for organic waste treatment. In order to expand our knowledge regarding microorganisms in the composting reactor, bacterial community structures in a variety of composting processes were examined by 16S rRNA gene (rDNA) clone analysis including denaturing gradient gel electrophoresis (DGGE), as a case study. As previously reported, the dominant bacteria consist of members of the order Bacillales in a typical composting condition with woodchips as the bulking agent. However, these aerobic bacteria decreased to 14%, and anaerobes or facultative anaerobes arose when the decomposition rate of organic compounds dropped following aggregation of the contents. In the composting reactor operated with plastic bottle flakes as bulking agent, the order Lactobacillales co-dominated with the Bacillales, regardless of reactor size, accounting for about 70% of the detected organisms during first week of the operation, gradually decreasing to about 30% with maturation of the composting process. Most species detected by clone analysis have not been cultivated, and may be VBNC (viable but non-culturable) species, implying symbiotic interactions among the microorganisms. In addition, the 16S rDNA-clone and DGGE methods are also introduced in this chapter.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Watanabe, K., Nagao, N., Toda, T. and Kurosawa, N (2008) Changes in bacterial community accompanied by aggregation in a fed-batch composting reactor . Curr Microbiol 56, 458–467.

    Article  CAS  PubMed  Google Scholar 

  2. Beffa, T., Blank, M., Lyon, P. F., Vogt, G., Marchiani, M., Fischer, J. L., and Aragano, M. (1996) Isolation of Thermus strains from hot composts (60–80°C). Appl Environ Microbiol 62, 1723–1727.

    CAS  PubMed  Google Scholar 

  3. Haruta, S., Kondo, M., Nakamura, K., Aiba, H., Ueno, S., Ishii, M., Igarashi, Y. (2002) Microbial community changes during organic solid waste treatment analyzed by double gradient-denaturing gradient gel electrophoresis and fluorescence in situ hybridization . Appl Microbiol Biotechnol 60, 224–231.

    Article  CAS  PubMed  Google Scholar 

  4. Narihiro, T., Takebayashi, S., and Hiraishi, A. (2004) Activity and phylogenetic composition of proteolytic Bacteria in mesophilic Fed-batch garbage composters . Microbes Environ 19, 292–300.

    Article  Google Scholar 

  5. Strom, P. F. (1985a) Identification of thermophilic bacteria in solid-waste composting. Appl Environ Microbiol 50, 906–913.

    CAS  PubMed  Google Scholar 

  6. Strom, P. F. (1985b) Effect of temperature on bacterial species diversity in thermophilic solid-waste composting. Appl Environ Microbiol 50, 899–905.

    CAS  PubMed  Google Scholar 

  7. Wang, Q., Garrity, G. M., Tiedje, J. M., and Cole, J. R. (2007) Naive Bayesian Classifier for rapid assignment of rRNA Sequences into the new bacterial taxonomy. Appl Environ Microbiol 73, 5261–5267.

    Article  CAS  PubMed  Google Scholar 

  8. Amann, R. I., Ludwig, W., and Schileifer, K-H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbial Rev 59, 143–169.

    CAS  Google Scholar 

  9. Kudo, T., and Ookuma, M. ed. (2004) Current Technology for Accessing Yet-Unexploit Microbial Resources. CMC Books, Tokyo, Japan (in Japanese).

    Google Scholar 

  10. Dees, P., and Ghiorse, W. (2001) Microbial diversity in hot synthetic compost as revealed by PCR-amplified rRNA sequences from cultivated isolates and extracted DNA. FEMS Microbiol Ecol 35, 207–216.

    Article  CAS  PubMed  Google Scholar 

  11. Neefs, J. M., and De Wachter, R. (1990) A proposal for the secondary structure of a variable area of eukaryotic small ribosomal subunit RNA involving the existence of a pseudoknot. Nucleic Acids Res 18, 5695–5704.

    Article  CAS  PubMed  Google Scholar 

  12. Stetzenbach, L. D., and Yates, M. V. (2003) The Dictionary of Environmental Microbiology. Academic press, San Diego, CA.

    Google Scholar 

  13. Myers, R. M., Maniatis, T., and Lerman, L. S. (1987) Dectection and localization of single base changes by denaturing gradient gel electrophoresis. Methods Enzymol 155, 501–527.

    Article  CAS  PubMed  Google Scholar 

  14. Nagao, N., Matsuyama, T., Yamamoto, H., Toda, T. (2003) A novel hybrid system of solid state and submerged fermentation with recycle for organic solid waste treatment. Process Biochem 39, 37–43.

    Article  CAS  Google Scholar 

  15. Nagao, N., Watanabe, K., Osa, S., Matsuyama, T., Kurosawa, N., Toda, T. (2008) Bacterial community and decomposition rate in long term fed-batch composting using woodchip and Polyethylene terephthalate (PET) as bulking agents. World J Microbiol Biotechnol 24, 1417–1424.

    Article  CAS  Google Scholar 

  16. Nagao, N., Osa, S., Matsuyama, T., Namiki, I., Yamamoto, H., and Toda, T. (2005) Optimization of washing rate in a hybrid recycling system of solid state and submerged fermentation. Process Biochem 40, 3321–3326.

    Article  CAS  Google Scholar 

  17. Kurosawa, N., Itoh, Y. H., and Itoh, T. (2005) Thermus kawarayensis sp. nov., a new member of the genus Thermus, isolated from Japanese hot springs Extremophiles 9, 81–84.

    Article  PubMed  Google Scholar 

  18. Altschul, S. F., Gish, W., Miller, W., Meyers, E. W., and Lipman, D. J. (1990) Basic local alignment search tool. J Mol Biol 215, 403–410.

    CAS  PubMed  Google Scholar 

  19. Ashelford, K. E., Chuzhanova, N. A., Fry, J. C., Jones, A. J., and Weightman, A. J. (2005) At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71, 7724–7736.

    Article  CAS  PubMed  Google Scholar 

  20. Singleton, D. R., Furlong, M. A., Rathbun, S. L., and Whitman, W. B. (2001) Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl Environ Microbiol 67, 4374–4376.

    Article  CAS  PubMed  Google Scholar 

  21. Higgins, D. (1998) Clustal W. Multiple sequence alignment. http://clustalw.genome.jp/ Cited 5 Feb 1998.

  22. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W; imprpving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.

    Article  CAS  PubMed  Google Scholar 

  23. Saitou, N., and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.

    CAS  PubMed  Google Scholar 

  24. Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368–376.

    Article  CAS  PubMed  Google Scholar 

  25. Felsenstein, J. (1993) PHYLIP (Phylogeny Inference Package) version 3.5c. http://evolution.genetics.washington.edu/phylip.html Distributed by the author, Department of Genetics, University of Washington.

  26. Ellis, R. J., Morgan, P., Weightman, A. J., and Fry, J. C. (2003) Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal-contaminated soil. Appl Environ Microbiol 69, 3223–3230.

    Article  CAS  PubMed  Google Scholar 

  27. Shibata, A., Goto, Y., and Nakajima, R. (2006) Use of SYBR Gold stain for enumerating bacteria and viruses in seawater samples. Bull Plankton Soc Jpn 53, 64–68 (In Japanese).

    Google Scholar 

  28. Pedro, M. S., Haruta, S., Hazaka, M., Shimada, R., Yoshida, C., Hiura, K., Ishii, M., and Igarashi, Y. (2001) Denaturing gradient gel electrophoresis analyses of microbial community from field-scale composter. J Biosci Bioeng 91, 159–165.

    Article  CAS  PubMed  Google Scholar 

  29. Ishii, K., Fukui, M., and Takii, S. (2000) Microbial succession during a composting process as evaluated by denaturing gradient gel electrophoresis analysis. J Appl Microbiol 89, 768–777.

    Article  CAS  PubMed  Google Scholar 

  30. Hemmi, H., Shimoyama, T., Nakayama, T., Hoshi, K., and Nishino, T. (2004) Molecular biological analysis of microflora in a garbage treatment process under thermoacidophilic conditions. J Biosci Bioeng 97, 119–126.

    CAS  PubMed  Google Scholar 

  31. Watanabe, K., Nagao, N., Toda, T., Kurosawa, N. (2009) The dominant bacteria shifted from the order “Lactobacillales” to Bacillales and Actinomycetales during a start-up period of large-scale, completely-mixed composting reactor using plastic bottle flakes as bulking agent. World J Microbiol Biotechnol 25, 803–811.

    Article  CAS  Google Scholar 

  32. Pedro, M. S., Haruta, S., Nakamura, K., et al. (2003) Isolation and characterization of predominant microorganisms during decomposition of waste materials in a field-scale composter. J Biosci Bioeng 95, 368–373

    CAS  PubMed  Google Scholar 

  33. Miyaguchi, H., Kurosawa, N., Toda, T. (2008) Real-time polymerase chain reaction assays for rapid detection and quantification of Noctiluca scintillans zoospore. Mar Biotechnol 10(2), 133–140

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by “University-Industry Joint Research” Project for Private Universities and a matching fund subsidy from MEXT (Ministry of Education, Culture, Sports, Science and Technology) of JAPAN, 2004–2008.

Author information

Authors and Affiliations

  1. Faculty of Engineering, Department of Environmental Engineering for Symbiosis, Soka University, 1–236, Hachioji, Tokyo, Japan

    Keiko Watanabe

  2. Faculty of Engineering, Department of Environmental Engineering for Symbiosis, Soka University, Hachioji, Tokyo, Japan

    Norio Nagao, Tatsuki Toda & Norio Kurosawa

Authors
  1. Keiko Watanabe
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Norio Nagao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Tatsuki Toda
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Norio Kurosawa
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Keiko Watanabe .

Editor information

Editors and Affiliations

  1. Bradford, 16704, U.S.A.

    Om V. Singh

  2. Edgewood Chemical Biological Center, US Army Medical Research, Blackhawk Road 5183, Aberdeen Proving Ground, 21010-5424, U.S.A.

    Steven P. Harvey

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer Science+Business Media B.V.

About this chapter

Cite this chapter

Watanabe, K., Nagao, N., Toda, T., Kurosawa, N. (2010). Bacterial Communities in Various Conditions of the Composting Reactor Revealed by 16S rDNA Clone Analysis and DGGE. In: Singh, O., Harvey, S. (eds) Sustainable Biotechnology. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-3295-9_8

Download citation

Publish with us

Policies and ethics

Search

Navigation